Mark DePristo 7a462399ce Fix GSA-529: Fix RODs for parallel read walkers ... -- TraverseReadsNano modified to read in all input data before invoking maps, so the input to TraverseReadsNano is a MapData object holding the sam record, the ref context, and the refmetadatatracker. -- Update ValidateRODForReads to be tree reducible, using synchronized map and explicitly sort the output map from locations -> counts in onTraversalDone -- Expanded integration tests to test nt 1, 2, 4.		2012-08-30 19:41:49 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Fix GSA-529: Fix RODs for parallel read walkers	2012-08-30 19:41:49 -04:00
test	Bugfix to compareTo and equals in GenomeLoc	2012-08-30 19:41:49 -04:00